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NAME

        runBlast.pl - A wrapper to run BLAST.

SYNOPSIS

        runBlast.pl [options]

OPTIONS

--flavor=name

WU-BLAST (WU), NCBI-BLAST (NCBI) or NCBI-BLAST+ (NCBI+) flavors of BLAST (default: WU)

--blast=program

BLAST program (blastn|blastp|blastx|tblastn|tblastx)

--database=name

BLAST database (an actual blast database or databases known to SMASH)

--query=string

BLAST query (a file, gene prediction id, assembly id or metagenome id)

--label=name

Prefix for the output file - final file will be <name>.<program> in the current working directory.

--evalue=num

E-value threshold for results to be included, passed to blast (default: 0.1)

--subjects=num

Maximum number of subjects per query to report, passed to blast (default: 10000)

--(no)tabular

Whether to use tabular output of BLAST (default: true)

--extra_args=string

Additional parameters passed to blast as they are. Use quotes if you use multiple parameters

--cpus=num

Number of cpus to use (default: 1)

DESCRIPTION

BLAST Query

If you specify a file using --query, then that will be used as the query. If you specify a gene prediction id, then the protein sequences from that gene prediction will be used. If you specify an assembly id, then the contig sequences from that assembly will be used. If you specify a metagenome id, then the read sequences from that metagenome will be used.

BLAST database

If you specify the prefix of an existing blast database using --database, then that will be used as the database.

Note

You should not specify the file extension. For example, for an NCBI blast formatted database named protdb, there will be at least three files called protdb.phr, protdb.pin and protdb.psq. You should only mention protdb and not protdb.phr or such.

If you want to use a database that SMASH knows about, such as the eggNOG protein database or the reference genomes database, which are located in the subdirectory called external in the data directory, you can just specify the name. Right now, SMASH knows about eggnog2 and reference_genomes.20100704.

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